Changelog

Source: NEWS.md

SCORPIUS 1.0.9

• Resubmission after babelwhale was removed from CRAN.

• DOCUMENTATION: Add vignette for working with AnnData objects.

• DOCUMENTATION: Add vignette for working with SingleCellExperiment objects.

• DOCUMENTATION: Create pkgdown site.

• DOCUMENTATION: Update citEntry to bibentry.

• DOCUMENTATION: Reduce execution time of examples by downscaling the example dataset.

SCORPIUS 1.0.8

CRAN release: 2021-06-09

• MINOR CHANGE: Allow adding row annotations to draw_trajectory_heatmap().

SCORPIUS 1.0.7 (2020-05-11)

CRAN release: 2020-05-11

Fix ahead of dplyr 1.0 release.

• MINOR CHANGE: substitute as.tbl_cube for reshape2::melt.

SCORPIUS 1.0.6 (2020-03-16)

CRAN release: 2020-03-16

Minor change

• Resubmission of SCORPIUS. SCORPIUS was removed from CRAN because dynwrap was removed from CRAN.

• Added a vignette for using SCORPIUS to analyse Seurat data.

SCORPIUS 1.0.5 (08-12-2019)

CRAN release: 2019-12-08

Major change

• Added a ti_scorpius() wrapper to SCORPIUS.

Minor change

• Use RANN::nn2() instead of own nearest neighbour functions.

• Remove deprecated functions.

• Use lmds instead of dyndimred.

SCORPIUS 1.0.4 (07-08-2019)

CRAN release: 2019-08-05

Minor changes

• Added extra customisation parameters to draw_trajectory_plot() and draw_trajectory_heatmap().

Optimisation

• Fixed internal function check_numeric_matrix() such that it does not run for ages when applied to a large sparse matrix.

• Minor improvement in infer_initial_trajectory() when calculating the distance from points to along candidate segments.

SCORPIUS 1.0.3 (27-05-2019)

CRAN release: 2019-05-27

Optimisation

• infer_trajectory(): Use princurve’s approx_points parameter, which greatly speeds up for trajectory inference for large number of samples.

Major changes

• Use dynutils’ calculate_distance() instead of correlation_distance() and euclidean_distance().

Documentation

• Vignettes were updated.

• Added cran-comments.md.

• Added recent news (inst/NEWS.md).

• Added citation information (inst/CITATION).

• Added support for sparsity in extract_modules() and dimensionality_reduction().

Minor changes

• Use scaling functions from dynutils (scale_minmax(), scale_quantile(), scale_uniform()).

• Expanded unit tests.

• Renormalise the original ginhoux data using dynnormaliser and rerun all vignettes.

• Moved cmdscale_withlandmarks() to dyndimred.

Bug fixes

• extract_modules(): smooth.spline() now requires at least 4 unique values.

Deprecation

• Deprecated unused functions evaluate_trajectory() and evaluate_dim_red(). Use dyneval::evaluate_ti_method() instead.

SCORPIUS 1.0.2 (2018-06-29)

CRAN release: 2018-06-29

• MINOR CHANGE: Depend on dynutils for distance functions.

• MAJOR CHANGE reduce_dimensionality(): Merge reduce_dimensionality_landmarked and reduce_dimensionality functions.

• REMOVAL: Removed outlier_filter(); there are much better scRNA-seq preprocessing pipelines in existance by now.

SCORPIUS 1.0.1 (2018-06-21)

• MINOR CHANGE: Update for princurve 2.0.2.

• REMOVAL: Removed deprecated functions infer.trajectory(), reduce.dimensionality, and so on.

• DOCUMENTATION: Various fixes.

• TESTING: Calculate code coverage on travis.

SCORPIUS 1.0.0 (2017-09-15)

• Initial release on CRAN.